activeCases	mspathCalculator-class
activeCases,mspathCalculator-method	mspathCalculator-class
activeCases-method	mspathCalculator-class
activeCases<-	mspathCalculator-class
activeCases<-,mspathCalculator,numeric-method	mspathCalculator-class
activeCases<--methods	mspathCalculator-class
addResult	addResult
addResult,runAnalyzer,runTime-method	runTime-class
alldone	alldone
batchsmoosh<-	batchsmoosh
batchsmoosh<-,ANY,ANY-method	batchsmoosh
batchsmoosh<-,list,list-method	batchsmoosh
batchsmoosh<-,mspath,mspath-method	batchsmoosh
batchsmoosh<-,mspathCalculator,mspathCalculator-method	batchsmoosh
batchsmoosh<-,mspathCoefficients,mspathCoefficients-method	batchsmoosh
batchsmoosh<-,mspathEstimatedCoefficients,mspathEstimatedCoefficients-method	batchsmoosh
batchsmoosh<-,mspathFull,mspathFull-method	batchsmoosh
batchsmoosh<--methods	batchsmoosh
bitMask	readingError-class
bitMask,readingError-method	readingError-class
boolMask	readingError-class
boolMask,readingError-method	readingError-class
calculate	calculate
calculate,mspathCalculator,ANY,ANY,ANY-method	calculate
calculate,mspathDistributedCalculator,numeric,missing,missing-method	calculate
calculate-methods	calculate
checkpoint	checkpoint
coef,mspath-method	mspath-class
coef,mspathCoefficients-method	mspathCoefficients-class
coef,mspathEstimatedCoefficients-method	mspathEstimatedCoefficients-class
coef,mspathFull-method	mspath-class
coef,readingError-method	readingError-class
cpuTime	runTime-class
cpuTime,runTime-method	runTime-class
deltamethod	deltamethod
done	done
done,mspathCalculator-method	done
done,mspathDistributedCalculator-method	done
done-methods	done
doneCode	mspath-internal
doTrials	doTrials
doubleType	mspath-internal
e2	e2
effort	effort
effort,mspathCalculator-method	effort
effort-methods	effort
endTime	runTime-class
endTime,runTime-method	runTime-class
estimateWork	estimateWork
estimateWork,mspathCalculator-method	estimateWork
estimateWork-methods	estimateWork
expit	expit
fixedSchedule	fixedSchedule
getlib	mspath-internal
integerType	mspath-internal
isAllFixed	isAllFixed-methods
isAllFixed,mspathCoefficients-method	mspathCoefficients-class
isAllFixed,mspathEstimatedCoefficients-method	isAllFixed-methods
isAllFixed-methods	isAllFixed-methods
job	runTime-class
job,runTime-method	runTime-class
logit	logit
master	master
matrixCoef	mspathCoefficients-class
matrixCoef,mspath-method	mspath-class
matrixCoef,mspathCoefficients-method	mspathCoefficients-class
matrixCoef-methods	mspathCoefficients-class
MatrixExp	MatrixExp
mean,readingError-method	readingError-class
minus2loglik	minus2loglik
minus2loglik,mspath-method	mspath-class
minus2loglik,mspathCalculator-method	minus2loglik
minus2loglik-methods	minus2loglik
mpirank	runTime-class
mpirank,runTime-method	runTime-class
mpirank<-	runTime-class
mpirank<-,runTime,numeric-method	runTime-class
mspath	mspath
mspath-class	mspath-class
mspath.check.consistency	mspath-internal
mspath.check.ematrix	mspath-internal
mspath.check.model	mspath-internal
mspath.check.qmatrix	mspath-internal
mspath.check.state	mspath-internal
mspath.check.times	mspath-internal
mspath.integerTime	mspath-internal
mspath.make.constraint	mspath-internal
mspath.process.covs	mspath-internal
mspath.process.path	mspath-internal
mspath.remove.overlap	mspath-internal
mspath.subset	subset
mspathAbstractCalculator-class	mspathCalculator-class
mspathCalculator	mspathCalculator
mspathCalculator-class	mspathCalculator-class
mspathCalculatorFromArgs	mspathCalculator
mspathCoefficients	mspathCoefficients-class
mspathCoefficients-class	mspathCoefficients-class
mspathDistributedCalculator	mspathDistributedCalculator
mspathDistributedCalculator-class	mspathDistributedCalculator-class
mspathDistributedCalculatorFactory	mspathDistributedCalculatorFactory
mspathEstimatedCoefficients	mspathEstimatedCoefficients-class
mspathEstimatedCoefficients-class	mspathEstimatedCoefficients-class
mspathFull-class	mspath-class
nActiveCases	mspathCalculator-class
nActiveCases,mspathCalculator-method	mspathCalculator-class
nActiveCases-methods	mspathCalculator-class
nBadNodes	mspath-class
nBadNodes,mspath-method	mspath-class
nBadNodes,mspathCalculator-method	mspathCalculator-class
nBadNodes-methods	mspath-class
nCases	mspath-class
nCases,mspath-method	mspath-class
nCases,mspathCalculator-method	mspathCalculator-class
nCases-methods	mspath-class
newRun	runAnalyzer-class
newRun,runAnalyzer-method	runAnalyzer-class
nGoodNodes	mspath-class
nGoodNodes,mspath-method	mspath-class
nGoodNodes,mspathCalculator-method	mspathCalculator-class
nGoodNodes-methods	mspath-class
nGoodPathNodes	mspath-class
nGoodPathNodes,mspath-method	mspath-class
nGoodPathNodes,mspathCalculator-method	mspathCalculator-class
nGoodPathNodes-methods	mspath-class
nGoodPaths	mspath-class
nGoodPaths,mspath-method	mspath-class
nGoodPaths,mspathCalculator-method	mspathCalculator-class
nGoodPaths-methods	mspath-class
optimizeWork	mspathCalculator-class
optimizeWork,mspathCalculator,numeric,numeric-method	mspathCalculator-class
optimizeWork-methods	mspathCalculator-class
optresults	mspath-class
optresults,mspath-method	mspath-class
optresults-methods	mspath-class
optresults<-	mspath-class
optresults<-,mspath-method	mspath-class
optresults<--methods	mspath-class
params<-	mspathCalculator-class
params<-,mspathCalculator,numeric-method	mspathCalculator-class
params<-,mspathDistributedCalculator,numeric-method	mspathDistributedCalculator-class
params<--methods	mspathCalculator-class
print,mspath-method	mspath-class
print,mspathCoefficients-method	mspathCoefficients-class
print,mspathEstimatedCoefficients-method	mspathEstimatedCoefficients-class
print,mspathFull-method	mspath-class
printFooter	mspath-class
printFooter,mspath-method	mspath-class
printFooter-methods	mspath-class
printOptim	mspath-internal
q2	q2
readingError	readingError-class
readingError-class	readingError-class
remoteTime<-	runTime-class
remoteTime<-,runTime,numeric-method	runTime-class
requestCode	mspath-internal
resultCode	mspath-internal
results	results
results,mspathCalculator-method	results
results-methods	results
root	mspath-internal
runAnalyzer	runAnalyzer-class
runAnalyzer-class	runAnalyzer-class
runeverywhere	runeverywhere
runTime	runTime
runTime-class	runTime-class
sd,mspath-method	mspath-class
sd,mspathCoefficients-method	mspathCoefficients-class
sd,mspathEstimatedCoefficients-method	mspathEstimatedCoefficients-class
sd,mspathFull-method	mspath-class
show,mspath-method	mspath-class
show,mspathCoefficients-method	mspathCoefficients-class
show,mspathEstimatedCoefficients-method	mspathEstimatedCoefficients-class
sim1	sim-data
sim2	sim-data
sim3	sim-data
simulateObservations	mspathCalculator-class
simulateObservations,mspathCalculator-method	mspathCalculator-class
simulateObservations-methods	mspathCalculator-class
slave	slave
smoosh	smoosh
smoosh,runAnalyzer-method	runAnalyzer-class
startTime	runTime-class
startTime,runTime-method	runTime-class
timeRequestCode	mspath-internal
trial	trial-class
trial-class	trial-class
useActualTimes	mspathCalculator-class
useActualTimes,mspathCalculator,numeric-method	mspathCalculator-class
useActualTimes-methods	mspathCalculator-class
waitTime	runTime-class
waitTime,runTime-method	runTime-class
wallTime	runTime-class
wallTime,runTime-method	runTime-class
